Rainfall variability, exacerbated by climate change, poses significant challenges to water resource management, particularly in regions prone to intense droughts and floods. The Greek islands, characterized by poor water potential, face interannual water supply issues dating back to their earliest habitation. Rainwater harvesting (RWH) systems emerge as a promising solution to address water scarcity in these regions. This study simulates RWH systems for two small Greek islands, Fourni and Nisyros, representing similar rainfall regimes. Multiple scenarios are explored, and system reliability is assessed in light of simulated daily rainfall time series incorporating climate change projections. Utilizing eight low/medium (RCP 4.5) and eight high (RCP 8.5) emission scenarios over a future 35-year period, the study evaluates system reliability based on model parameters (collection area: 40 to 140 m2, rainwater tank volume: 5 to 30 m3, number of household members: 2, 3), with 30% coverage of total daily water demand (180 L/d). Negligible evapotranspiration effects are assumed due to closed-type tanks. Results indicate that the RWH system demonstrates high efficiency in general. The investigation for the future period revealed that the system’s performance varies, with instances where daily demand targets are not met, even with a 30 m3 tank. This research underscores the potential of RWH systems as a cost-effective “green” solution, particularly in regions with deficient rainfall regimes. It highlights the importance of localized water management strategies, reducing reliance on mainland water transportation, and assisting desalination unit operations. In conclusion, this study contributes to the assessment of RWH systems, demonstrating their viability as a sustainable water management solution in regions facing water scarcity, contingent on local rainfall conditions and system design parameters.